In this report, we will study the Splicing noise for specific RBP/NMD projects. This is an extension of the analysis from Splicing_Analysis_Results.Rmd, please refer to that report to understand the methodology. Based on results from that analysis, we will focus this report in the following RBPs:
The figure that inspired these studied RBPs:
Figure 1.1: Studied RBPs
An example of the novel junctions table obtained from the analysis can be seen in the following table:
| Novel jun. ID | Novel type | Cluster | Sequence | Distance [bp] |
|---|---|---|---|---|
| 363481 | novel_acceptor | case | exon | 18 |
| 961436 | novel_acceptor | control | intron | -46 |
| 358517 | novel_acceptor | case | exon | 53 |
| 2135689 | novel_acceptor | control | exon | 31 |
| 1603789 | novel_acceptor | case | exon | 24 |
| 790311 | novel_acceptor | case | exon | 5 |
| 422853 | novel_acceptor | control | exon | 4 |
| 1126415 | novel_donor | case | intron | -81 |
| 1478437 | novel_acceptor | control | exon | 3 |
| 2126164 | novel_acceptor | case | intron | -34 |
The distances graph is generated by counting the number of unique novel junctions at any given distance of the reference splicing site. From the list of novel junctions associated to common reference introns, we group by novel_type and cluster, count the number of entries for each distance within 30 bp into both intron and exon sequence, and represent the data in a histogram.
For each project, different graphical representations will be presented. First, we present a histogram of the different distance values between -30 and 30 bp, with the case bars stacked on top of the control bars:
However, this representation does not allow for an easy comparison between cases and controls because of the bar stacking. To do so, we split the graph in two more facets to represent each cluster by its own (notice the different Y-axis for the two rows):
If we focus on the difference in the number of unique novel junctions between cases and controls, the last graph represent the histogram resulting from subtracting the control distances from the case distances:
To generate the modulo 3 graphs, we first filter by those distances smaller than 100 bp in either direction. Then, we group by novel_type and cluster, and calculate the distance in modulo 3 (i.e. the remainder from the division of the distance by 3). Once we have all novel junctions split in the four different categories with their distances in modulo 3, we calculate the percentage that each modulo 3 represents in each category. Thus, for each category:
\[ \text{mod.0 }\% = \frac{\# 0}{\#0 + \#1 + \#2}*100\%\qquad\quad \text{mod.1 }\% = \frac{\# 1}{\#0 + \#1 + \#2}*100\%\qquad\quad \text{mod.2 }\% = \frac{\# 2}{\#0 + \#1 + \#2}*100\% \]
Here, \(\#X\) represents the number of novel junctions at a modulo 3 distance equal to \(X\). For example, from the information of the following table, we can focus on the control acceptor group, where we observe three 0s, one 1 and one 2:
| Novel jun. ID | Novel type | Cluster | Sequence | Distance [bp] | Mod3 distance [bp] |
|---|---|---|---|---|---|
| case acceptor | |||||
| 1754423 | novel_acceptor | control | exon | 3 | 0 |
| 1863847 | novel_acceptor | case | exon | 78 | 0 |
| 2739925 | novel_acceptor | case | exon | 3 | 0 |
| case donor | |||||
| 1360358 | novel_acceptor | control | intron | -82 | 1 |
| control acceptor | |||||
| 2262507 | novel_donor | control | intron | -29 | 2 |
| 1050197 | novel_donor | case | exon | 7 | 1 |
| 973839 | novel_acceptor | case | exon | 24 | 0 |
| 317456 | novel_acceptor | control | intron | -27 | 0 |
| 2029914 | novel_acceptor | control | exon | 15 | 0 |
| control donor | |||||
| 287795 | novel_acceptor | control | intron | -25 | 1 |
Thus, the calculated percentage are:
\[ \text{mod.0 }\% = 60\%\qquad\quad \text{mod.1 }\% = 20\%\qquad\quad \text{mod.2 }\% = 20\% \]
Additionally, we can further group the novel junctions by their intron/exon sequence, resulting a total of 8 categories, where the same calculation of percentages can be applied:
| Novel jun. ID | Novel type | Cluster | Sequence | Distance [bp] | Mod3 distance [bp] |
|---|---|---|---|---|---|
| case acceptor exon | |||||
| 1023682 | novel_acceptor | control | exon | 4 | 1 |
| 736164 | novel_donor | case | exon | 27 | 0 |
| 2730860 | novel_donor | case | exon | 48 | 0 |
| case donor exon | |||||
| 2300571 | novel_acceptor | control | intron | -19 | 1 |
| 1502232 | novel_acceptor | control | exon | 5 | 2 |
| control acceptor exon | |||||
| 1491329 | novel_acceptor | case | exon | 4 | 1 |
| 2559252 | novel_donor | control | intron | -10 | 1 |
| 405412 | novel_donor | control | intron | -7 | 1 |
| control acceptor intron | |||||
| 2628084 | novel_acceptor | case | exon | 10 | 1 |
| control donor exon | |||||
| 126904 | novel_donor | control | intron | -5 | 2 |
| 522911 | novel_donor | control | exon | 23 | 2 |
| control donor intron | |||||
| 1297076 | novel_acceptor | case | exon | 5 | 2 |
| 427027 | novel_acceptor | control | exon | 4 | 1 |
| 453607 | novel_donor | control | exon | 10 | 1 |
| 857551 | novel_donor | control | intron | -4 | 1 |
With the previous tables in mind, we represent them in three different ways. The first one just represents the number of unique novel junctions for each modulo 3 distance where \(abs(distance) <= 100\).
We also represent the percentage that each that each distance in modulo 3 represents when grouped by novel_type (i.e. acceptor/donor) and cluster (i.e. case/control).
Lastly, we represent the same data as before but taking into consideration whether it is located in the intronic or exonic sequence:
To represent the difference in MaxEntScan scores (MES), we subtract the MaxEntScan score of the annotated intron to the MaxEntScan score of a novel junction at each splice site. We obtain a table like the following, and represent the density plot of the different values for delta_ss5score and delta_ss3score:
\[ \text{Delta MES}^{5'} = \text{MES}_{ref}^{5'}-\text{MES}_{novel}^{5'}\qquad\qquad\text{Delta MES}^{3'} = \text{MES}_{ref}^{3'}-\text{MES}_{novel}^{3'} \]
Example table with the Delta MES data:
| Novel jun. ID | Ref. jun. ID | Ref. ss5score | Ref. ss3score | Novel ss5score | Novel ss3score | Delta ss5score | Delta ss3score |
|---|---|---|---|---|---|---|---|
| 1935070 | 1935302 | 7.83 | 9.47 | -5.84 | 9.47 | 13.67 | 0.00 |
| 2598431 | 2598425 | 9.09 | 7.77 | -7.04 | 7.77 | 16.13 | 0.00 |
| 2826616 | 2826619 | 10.36 | 8.88 | 9.10 | 8.88 | 1.26 | 0.00 |
| 1533056 | 1533051 | 9.66 | 8.32 | 9.66 | 6.39 | 0.00 | 1.93 |
| 2745194 | 2745195 | 8.30 | 8.63 | 8.30 | 4.38 | 0.00 | 4.25 |
| 1263411 | 1263491 | 7.94 | 8.57 | 7.94 | 6.01 | 0.00 | 2.56 |
| 1274817 | 1274816 | 10.07 | 8.65 | 10.07 | 2.70 | 0.00 | 5.95 |
| 1042659 | 1042661 | 9.16 | 11.54 | 5.87 | 11.54 | 3.29 | 0.00 |
| 2675925 | 2675913 | 10.07 | 7.18 | 10.07 | 4.74 | 0.00 | 2.44 |
| 584316 | 584306 | 10.10 | 8.76 | 10.10 | 5.64 | 0.00 | 3.12 |
As for the visual representations, the difference between the MaxEntScan scores for each splice site is shown in the X-axis. The Y-axis represents the kernel density estimate (smoothed version of a histogram). The fill colour represents cases vs. controls.
Additionally, we can also represent the difference in the kernel density estimate between case and control:
The Mis-Splicing Ratio (MSR) is calculated in the data-analysis pipeline for each annotated intron found in the project samples. More information about the mis-splicing ratio can be found in the Splicing Analysis Results report. To visualize this data, we represent the density plot for MSR at the different splice sites (i.e. donor or acceptor). Example table with the MSR data:
| Ref. jun, ID | Cluster | Ref. type | MSR Donor | MSR Acceptor |
|---|---|---|---|---|
| 522301 | case | never | 0.000 | 0.000 |
| 1673247 | case | never | 0.000 | 0.000 |
| 799707 | case | never | 0.000 | 0.000 |
| 164540 | case | never | 0.000 | 0.000 |
| 561682 | case | both | 0.008 | 0.016 |
| 1729913 | case | never | 0.000 | 0.000 |
| 844081 | case | never | 0.000 | 0.000 |
| 1863690 | case | never | 0.000 | 0.000 |
| 2310284 | control | never | 0.000 | 0.000 |
| 589320 | control | never | 0.000 | 0.000 |
We represent both the distribution of mis-splicing ratio (MSR) at the donor site and the acceptor site. The X-axis represents the MSR, while the Y-axis represents the kernel density estimate.
Note that the distributions have a discontinuity at \(x=0.05\) to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis will also be present if the difference between the two sample types exceeds a predefined threshold.
Under the Stats subsection, we will study different statistics of the annotated introns and novel junctions:
Unique annotated introns: number of annotated introns classified as never mis-spliced, mis-spliced at acceptor end, donor end or both. It is represented by cluster, so that we can study the variation in the number and percentage of never mis-spliced annotated introns.
Reads - annotated introns: total reads associated to annotated introns and the percentage that they represent against the total read depth.
Reads - novel junctions: total reads associated to novel junctions and the percentage that they represent against the total read depth. Results are separated by cluster.
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 18270 | 16.62 |
| acceptor | control | 109950 | 14086 | 12.81 |
| both | case | 109950 | 11261 | 10.24 |
| both | control | 109950 | 6434 | 5.85 |
| donor | case | 109950 | 12456 | 11.33 |
| donor | control | 109950 | 8886 | 8.08 |
| never | case | 109950 | 67963 | 61.81 |
| never | control | 109950 | 80544 | 73.26 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 95581047 | 57055044 | 59.69 |
| control | 109950 | 65858978 | 42355364 | 64.31 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 73698 | 40563 | 95581047 | 131151 | 0.14 |
| case | novel_donor | 73698 | 33135 | 95581047 | 109513 | 0.11 |
| control | novel_acceptor | 45976 | 26222 | 65858978 | 79648 | 0.12 |
| control | novel_donor | 45976 | 19754 | 65858978 | 59477 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 19769 | 17.98 |
| acceptor | control | 109950 | 13665 | 12.43 |
| both | case | 109950 | 9004 | 8.19 |
| both | control | 109950 | 6063 | 5.51 |
| donor | case | 109950 | 9367 | 8.52 |
| donor | control | 109950 | 8655 | 7.87 |
| never | case | 109950 | 71810 | 65.31 |
| never | control | 109950 | 81567 | 74.19 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 139108128 | 66096990 | 47.51 |
| control | 109950 | 103415982 | 62586996 | 60.52 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 65546 | 40372 | 139108128 | 186928 | 0.13 |
| case | novel_donor | 65546 | 25174 | 139108128 | 109366 | 0.08 |
| control | novel_acceptor | 44508 | 25403 | 103415982 | 108110 | 0.10 |
| control | novel_donor | 44508 | 19105 | 103415982 | 77954 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 21559 | 19.61 |
| acceptor | control | 109950 | 15553 | 14.15 |
| both | case | 109950 | 11286 | 10.26 |
| both | control | 109950 | 7235 | 6.58 |
| donor | case | 109950 | 10515 | 9.56 |
| donor | control | 109950 | 9359 | 8.51 |
| never | case | 109950 | 66590 | 60.56 |
| never | control | 109950 | 77803 | 70.76 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 131286007 | 67739458 | 51.60 |
| control | 109950 | 102950731 | 59580485 | 57.87 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 78217 | 47601 | 131286007 | 196876 | 0.15 |
| case | novel_donor | 78217 | 30616 | 131286007 | 123442 | 0.09 |
| control | novel_acceptor | 51788 | 29903 | 102950731 | 108941 | 0.11 |
| control | novel_donor | 51788 | 21885 | 102950731 | 78812 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 18610 | 16.93 |
| acceptor | control | 109950 | 15717 | 14.29 |
| both | case | 109950 | 12184 | 11.08 |
| both | control | 109950 | 7109 | 6.47 |
| donor | case | 109950 | 10436 | 9.49 |
| donor | control | 109950 | 9288 | 8.45 |
| never | case | 109950 | 68720 | 62.50 |
| never | control | 109950 | 77836 | 70.79 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 87390817 | 47804029 | 54.70 |
| control | 109950 | 90031602 | 55948250 | 62.14 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 78313 | 45366 | 87390817 | 185465 | 0.21 |
| case | novel_donor | 78313 | 32947 | 87390817 | 143669 | 0.16 |
| control | novel_acceptor | 51396 | 29865 | 90031602 | 102086 | 0.11 |
| control | novel_donor | 51396 | 21531 | 90031602 | 72824 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 17425 | 15.85 |
| acceptor | control | 109950 | 17890 | 16.27 |
| both | case | 109950 | 9299 | 8.46 |
| both | control | 109950 | 9824 | 8.93 |
| donor | case | 109950 | 10320 | 9.39 |
| donor | control | 109950 | 10512 | 9.56 |
| never | case | 109950 | 72906 | 66.31 |
| never | control | 109950 | 71724 | 65.23 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 113084161 | 72796158 | 64.37 |
| control | 109950 | 123546347 | 80521666 | 65.18 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 63140 | 36386 | 113084161 | 137440 | 0.12 |
| case | novel_donor | 63140 | 26754 | 113084161 | 103469 | 0.09 |
| control | novel_acceptor | 66081 | 38025 | 123546347 | 143463 | 0.12 |
| control | novel_donor | 66081 | 28056 | 123546347 | 107709 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 15859 | 14.42 |
| acceptor | control | 109950 | 16478 | 14.99 |
| both | case | 109950 | 8045 | 7.32 |
| both | control | 109950 | 8585 | 7.81 |
| donor | case | 109950 | 10180 | 9.26 |
| donor | control | 109950 | 10050 | 9.14 |
| never | case | 109950 | 75866 | 69.00 |
| never | control | 109950 | 74837 | 68.06 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 91520968 | 56599674 | 61.84 |
| control | 109950 | 95867805 | 61574898 | 64.23 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 55870 | 31557 | 91520968 | 106523 | 0.12 |
| case | novel_donor | 55870 | 24313 | 91520968 | 84947 | 0.09 |
| control | novel_acceptor | 58648 | 33384 | 95867805 | 114395 | 0.12 |
| control | novel_donor | 58648 | 25264 | 95867805 | 86835 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 15020 | 13.66 |
| acceptor | control | 109950 | 15541 | 14.13 |
| both | case | 109950 | 7748 | 7.05 |
| both | control | 109950 | 7891 | 7.18 |
| donor | case | 109950 | 9413 | 8.56 |
| donor | control | 109950 | 9775 | 8.89 |
| never | case | 109950 | 77769 | 70.73 |
| never | control | 109950 | 76743 | 69.80 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 81752442 | 50647498 | 61.95 |
| control | 109950 | 88157283 | 55672338 | 63.15 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 52661 | 29889 | 81752442 | 96038 | 0.12 |
| case | novel_donor | 52661 | 22772 | 81752442 | 74037 | 0.09 |
| control | novel_acceptor | 54588 | 30897 | 88157283 | 100494 | 0.11 |
| control | novel_donor | 54588 | 23691 | 88157283 | 79025 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 17613 | 16.02 |
| acceptor | control | 109950 | 17986 | 16.36 |
| both | case | 109950 | 9380 | 8.53 |
| both | control | 109950 | 9527 | 8.66 |
| donor | case | 109950 | 10326 | 9.39 |
| donor | control | 109950 | 10487 | 9.54 |
| never | case | 109950 | 72631 | 66.06 |
| never | control | 109950 | 71950 | 65.44 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 100754176 | 64596002 | 64.11 |
| control | 109950 | 138180087 | 86870723 | 62.87 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 63644 | 36881 | 100754176 | 128834 | 0.13 |
| case | novel_donor | 63644 | 26763 | 100754176 | 95041 | 0.09 |
| control | novel_acceptor | 65324 | 37777 | 138180087 | 149333 | 0.11 |
| control | novel_donor | 65324 | 27547 | 138180087 | 112111 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 18788 | 17.09 |
| acceptor | control | 109950 | 15810 | 14.38 |
| both | case | 109950 | 10451 | 9.51 |
| both | control | 109950 | 7681 | 6.99 |
| donor | case | 109950 | 10916 | 9.93 |
| donor | control | 109950 | 9693 | 8.82 |
| never | case | 109950 | 69795 | 63.48 |
| never | control | 109950 | 76766 | 69.82 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 98785090 | 66624975 | 67.44 |
| control | 109950 | 78934064 | 51369435 | 65.08 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 70863 | 40733 | 98785090 | 138015 | 0.14 |
| case | novel_donor | 70863 | 30130 | 98785090 | 105799 | 0.11 |
| control | novel_acceptor | 53565 | 30753 | 78934064 | 94553 | 0.12 |
| control | novel_donor | 53565 | 22812 | 78934064 | 71888 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 15760 | 14.33 |
| acceptor | control | 109950 | 14567 | 13.25 |
| both | case | 109950 | 7073 | 6.43 |
| both | control | 109950 | 6396 | 5.82 |
| donor | case | 109950 | 8872 | 8.07 |
| donor | control | 109950 | 8766 | 7.97 |
| never | case | 109950 | 78245 | 71.16 |
| never | control | 109950 | 80221 | 72.96 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 75910349 | 44094079 | 58.09 |
| control | 109950 | 74988044 | 45380161 | 60.52 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 50693 | 29843 | 75910349 | 93607 | 0.12 |
| case | novel_donor | 50693 | 20850 | 75910349 | 65790 | 0.09 |
| control | novel_acceptor | 46756 | 27067 | 74988044 | 85697 | 0.11 |
| control | novel_donor | 46756 | 19689 | 74988044 | 61378 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 18354 | 16.69 |
| acceptor | control | 109950 | 17072 | 15.53 |
| both | case | 109950 | 9600 | 8.73 |
| both | control | 109950 | 8843 | 8.04 |
| donor | case | 109950 | 11041 | 10.04 |
| donor | control | 109950 | 10025 | 9.12 |
| never | case | 109950 | 70955 | 64.53 |
| never | control | 109950 | 74010 | 67.31 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 107100947 | 67220366 | 62.76 |
| control | 109950 | 104974265 | 68643820 | 65.39 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 66654 | 38375 | 107100947 | 136058 | 0.13 |
| case | novel_donor | 66654 | 28279 | 107100947 | 104238 | 0.10 |
| control | novel_acceptor | 60402 | 35054 | 104974265 | 124731 | 0.12 |
| control | novel_donor | 60402 | 25348 | 104974265 | 90643 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 18183 | 16.54 |
| acceptor | control | 109950 | 16339 | 14.86 |
| both | case | 109950 | 10773 | 9.80 |
| both | control | 109950 | 7938 | 7.22 |
| donor | case | 109950 | 10867 | 9.88 |
| donor | control | 109950 | 9806 | 8.92 |
| never | case | 109950 | 70127 | 63.78 |
| never | control | 109950 | 75867 | 69.00 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 120642911 | 73861148 | 61.22 |
| control | 109950 | 127058916 | 84110749 | 66.20 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 71101 | 40621 | 120642911 | 150627 | 0.12 |
| case | novel_donor | 71101 | 30480 | 120642911 | 116941 | 0.10 |
| control | novel_acceptor | 56579 | 32499 | 127058916 | 127074 | 0.10 |
| control | novel_donor | 56579 | 24080 | 127058916 | 98371 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 36429 | 33.13 |
| acceptor | control | 109950 | 18224 | 16.57 |
| both | case | 109950 | 34316 | 31.21 |
| both | control | 109950 | 10856 | 9.87 |
| donor | case | 109950 | 7396 | 6.73 |
| donor | control | 109950 | 11068 | 10.07 |
| never | case | 109950 | 31809 | 28.93 |
| never | control | 109950 | 69802 | 63.49 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 133197366 | 70652393 | 53.04 |
| control | 109950 | 126533708 | 81822502 | 64.66 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 289498 | 216314 | 133197366 | 995257 | 0.75 |
| case | novel_donor | 289498 | 73184 | 133197366 | 260535 | 0.20 |
| control | novel_acceptor | 71583 | 40904 | 126533708 | 158410 | 0.13 |
| control | novel_donor | 71583 | 30679 | 126533708 | 122555 | 0.10 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 27909 | 25.38 |
| acceptor | control | 109950 | 18108 | 16.47 |
| both | case | 109950 | 16837 | 15.31 |
| both | control | 109950 | 9740 | 8.86 |
| donor | case | 109950 | 11808 | 10.74 |
| donor | control | 109950 | 10428 | 9.48 |
| never | case | 109950 | 53396 | 48.56 |
| never | control | 109950 | 71674 | 65.19 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 171167876 | 91151237 | 53.25 |
| control | 109950 | 140949277 | 83680600 | 59.37 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 112924 | 71882 | 171167876 | 264601 | 0.15 |
| case | novel_donor | 112924 | 41042 | 171167876 | 166485 | 0.10 |
| control | novel_acceptor | 66349 | 38262 | 140949277 | 158158 | 0.11 |
| control | novel_donor | 66349 | 28087 | 140949277 | 116118 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 22865 | 20.80 |
| acceptor | control | 109950 | 15927 | 14.49 |
| both | case | 109950 | 10591 | 9.63 |
| both | control | 109950 | 7631 | 6.94 |
| donor | case | 109950 | 10165 | 9.25 |
| donor | control | 109950 | 9453 | 8.60 |
| never | case | 109950 | 66329 | 60.33 |
| never | control | 109950 | 76939 | 69.98 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 112510049 | 64700999 | 57.51 |
| control | 109950 | 122011801 | 81627934 | 66.90 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 75020 | 47078 | 112510049 | 169880 | 0.15 |
| case | novel_donor | 75020 | 27942 | 112510049 | 100554 | 0.09 |
| control | novel_acceptor | 54596 | 31594 | 122011801 | 119731 | 0.10 |
| control | novel_donor | 54596 | 23002 | 122011801 | 90714 | 0.07 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 17301 | 15.74 |
| acceptor | control | 109950 | 14640 | 13.32 |
| both | case | 109950 | 9738 | 8.86 |
| both | control | 109950 | 6722 | 6.11 |
| donor | case | 109950 | 11024 | 10.03 |
| donor | control | 109950 | 9241 | 8.40 |
| never | case | 109950 | 71887 | 65.38 |
| never | control | 109950 | 79347 | 72.17 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 134926056 | 71707770 | 53.15 |
| control | 109950 | 130648179 | 82068661 | 62.82 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 65685 | 37169 | 134926056 | 152506 | 0.11 |
| case | novel_donor | 65685 | 28516 | 134926056 | 113426 | 0.08 |
| control | novel_acceptor | 48974 | 27806 | 130648179 | 146489 | 0.11 |
| control | novel_donor | 48974 | 21168 | 130648179 | 107454 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 15878 | 14.44 |
| acceptor | control | 109950 | 13582 | 12.35 |
| both | case | 109950 | 7066 | 6.43 |
| both | control | 109950 | 5955 | 5.42 |
| donor | case | 109950 | 9781 | 8.90 |
| donor | control | 109950 | 8757 | 7.96 |
| never | case | 109950 | 77225 | 70.24 |
| never | control | 109950 | 81656 | 74.27 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 80269690 | 46414907 | 57.82 |
| control | 109950 | 71066567 | 42863013 | 60.31 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 52297 | 30224 | 80269690 | 93808 | 0.12 |
| case | novel_donor | 52297 | 22073 | 80269690 | 72979 | 0.09 |
| control | novel_acceptor | 43798 | 24870 | 71066567 | 80646 | 0.11 |
| control | novel_donor | 43798 | 18928 | 71066567 | 62007 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 17607 | 16.01 |
| acceptor | control | 109950 | 16315 | 14.84 |
| both | case | 109950 | 9198 | 8.37 |
| both | control | 109950 | 8259 | 7.51 |
| donor | case | 109950 | 10187 | 9.27 |
| donor | control | 109950 | 9547 | 8.68 |
| never | case | 109950 | 72958 | 66.36 |
| never | control | 109950 | 75829 | 68.97 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 151041133 | 86623869 | 57.35 |
| control | 109950 | 123467051 | 73104575 | 59.21 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 62842 | 36443 | 151041133 | 172136 | 0.11 |
| case | novel_donor | 62842 | 26399 | 151041133 | 127177 | 0.08 |
| control | novel_acceptor | 56647 | 32910 | 123467051 | 143879 | 0.12 |
| control | novel_donor | 56647 | 23737 | 123467051 | 103935 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 16979 | 15.44 |
| acceptor | control | 109950 | 16478 | 14.99 |
| both | case | 109950 | 8517 | 7.75 |
| both | control | 109950 | 8585 | 7.81 |
| donor | case | 109950 | 9971 | 9.07 |
| donor | control | 109950 | 10050 | 9.14 |
| never | case | 109950 | 74483 | 67.74 |
| never | control | 109950 | 74837 | 68.06 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 97561814 | 62255240 | 63.81 |
| control | 109950 | 95867805 | 61574898 | 64.23 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 59168 | 34294 | 97561814 | 119422 | 0.12 |
| case | novel_donor | 59168 | 24874 | 97561814 | 86686 | 0.09 |
| control | novel_acceptor | 58648 | 33384 | 95867805 | 114395 | 0.12 |
| control | novel_donor | 58648 | 25264 | 95867805 | 86835 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 20302 | 18.46 |
| acceptor | control | 109950 | 16315 | 14.84 |
| both | case | 109950 | 11993 | 10.91 |
| both | control | 109950 | 8259 | 7.51 |
| donor | case | 109950 | 10718 | 9.75 |
| donor | control | 109950 | 9547 | 8.68 |
| never | case | 109950 | 66937 | 60.88 |
| never | control | 109950 | 75829 | 68.97 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 148180187 | 79615414 | 53.73 |
| control | 109950 | 123467051 | 73104575 | 59.21 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 78549 | 46737 | 148180187 | 203284 | 0.14 |
| case | novel_donor | 78549 | 31812 | 148180187 | 146294 | 0.10 |
| control | novel_acceptor | 56647 | 32910 | 123467051 | 143879 | 0.12 |
| control | novel_donor | 56647 | 23737 | 123467051 | 103935 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 16566 | 15.07 |
| acceptor | control | 109950 | 14086 | 12.81 |
| both | case | 109950 | 8810 | 8.01 |
| both | control | 109950 | 6434 | 5.85 |
| donor | case | 109950 | 10964 | 9.97 |
| donor | control | 109950 | 8886 | 8.08 |
| never | case | 109950 | 73610 | 66.95 |
| never | control | 109950 | 80544 | 73.26 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 80807406 | 49789650 | 61.62 |
| control | 109950 | 65858978 | 42355364 | 64.31 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 60820 | 33896 | 80807406 | 111289 | 0.14 |
| case | novel_donor | 60820 | 26924 | 80807406 | 87885 | 0.11 |
| control | novel_acceptor | 45976 | 26222 | 65858978 | 79648 | 0.12 |
| control | novel_donor | 45976 | 19754 | 65858978 | 59477 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 17538 | 15.95 |
| acceptor | control | 109950 | 16315 | 14.84 |
| both | case | 109950 | 9245 | 8.41 |
| both | control | 109950 | 8259 | 7.51 |
| donor | case | 109950 | 10300 | 9.37 |
| donor | control | 109950 | 9547 | 8.68 |
| never | case | 109950 | 72867 | 66.27 |
| never | control | 109950 | 75829 | 68.97 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 135803280 | 77474141 | 57.05 |
| control | 109950 | 123467051 | 73104575 | 59.21 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 62783 | 36110 | 135803280 | 152543 | 0.11 |
| case | novel_donor | 62783 | 26673 | 135803280 | 111983 | 0.08 |
| control | novel_acceptor | 56647 | 32910 | 123467051 | 143879 | 0.12 |
| control | novel_donor | 56647 | 23737 | 123467051 | 103935 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 15632 | 14.22 |
| acceptor | control | 109950 | 15541 | 14.13 |
| both | case | 109950 | 7820 | 7.11 |
| both | control | 109950 | 7891 | 7.18 |
| donor | case | 109950 | 9761 | 8.88 |
| donor | control | 109950 | 9775 | 8.89 |
| never | case | 109950 | 76737 | 69.79 |
| never | control | 109950 | 76743 | 69.80 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 87700972 | 55703851 | 63.52 |
| control | 109950 | 88157283 | 55672338 | 63.15 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 54326 | 30946 | 87700972 | 101282 | 0.12 |
| case | novel_donor | 54326 | 23380 | 87700972 | 78126 | 0.09 |
| control | novel_acceptor | 54588 | 30897 | 88157283 | 100494 | 0.11 |
| control | novel_donor | 54588 | 23691 | 88157283 | 79025 | 0.09 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 16595 | 15.09 |
| acceptor | control | 109950 | 16787 | 15.27 |
| both | case | 109950 | 8051 | 7.32 |
| both | control | 109950 | 8441 | 7.68 |
| donor | case | 109950 | 9968 | 9.07 |
| donor | control | 109950 | 9776 | 8.89 |
| never | case | 109950 | 75336 | 68.52 |
| never | control | 109950 | 74946 | 68.16 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 100953374 | 63435477 | 62.84 |
| control | 109950 | 110552729 | 70304787 | 63.59 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 56388 | 32491 | 100953374 | 113971 | 0.11 |
| case | novel_donor | 56388 | 23897 | 100953374 | 84617 | 0.08 |
| control | novel_acceptor | 58421 | 33887 | 110552729 | 123550 | 0.11 |
| control | novel_donor | 58421 | 24534 | 110552729 | 90550 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 21429 | 19.49 |
| acceptor | control | 109950 | 16352 | 14.87 |
| both | case | 109950 | 14960 | 13.61 |
| both | control | 109950 | 7395 | 6.73 |
| donor | case | 109950 | 13449 | 12.23 |
| donor | control | 109950 | 9541 | 8.68 |
| never | case | 109950 | 60112 | 54.67 |
| never | control | 109950 | 76662 | 69.72 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 114070552 | 72091127 | 63.20 |
| control | 109950 | 117220176 | 78940705 | 67.34 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 98532 | 56033 | 114070552 | 221927 | 0.19 |
| case | novel_donor | 98532 | 42499 | 114070552 | 183352 | 0.16 |
| control | novel_acceptor | 54022 | 31483 | 117220176 | 119271 | 0.10 |
| control | novel_donor | 54022 | 22539 | 117220176 | 89354 | 0.08 |
ENCODE experiment summary:
Information:
Samples analysed:
| Mis-spliced site | Cluster | # Annotated introns | # Ann. introns by splice site | Percent [%] |
|---|---|---|---|---|
| acceptor | case | 109950 | 22677 | 20.62 |
| acceptor | control | 109950 | 16339 | 14.86 |
| both | case | 109950 | 14993 | 13.64 |
| both | control | 109950 | 7938 | 7.22 |
| donor | case | 109950 | 12787 | 11.63 |
| donor | control | 109950 | 9806 | 8.92 |
| never | case | 109950 | 59493 | 54.11 |
| never | control | 109950 | 75867 | 69.00 |
| Cluster | # Annotated introns | # Reads in cluster | # Ann. intron reads | Percentage [%] |
|---|---|---|---|---|
| case | 109950 | 121889488 | 75178667 | 61.68 |
| control | 109950 | 127058916 | 84110749 | 66.20 |
| Cluster | Novel type | # Novel junctions | # Novel junc. in splice site | # Reads in cluster | # Novel junc. reads | Percentage [%] |
|---|---|---|---|---|---|---|
| case | novel_acceptor | 99769 | 58477 | 121889488 | 223557 | 0.18 |
| case | novel_donor | 99769 | 41292 | 121889488 | 182588 | 0.15 |
| control | novel_acceptor | 56579 | 32499 | 127058916 | 127074 | 0.10 |
| control | novel_donor | 56579 | 24080 | 127058916 | 98371 | 0.08 |